Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

By Devin Coleman-Derr, D. Desgarennes, Citlali Fonseca-García, Stephen Gross, S. Clingenpeel, Tanja Woyke, G. North, Axel Visel, L. Partida-Martínez, Susannah Tringe. New Phytologist, 2015

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Summary Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave–microbe interactions.

Subfields: Cell Biology, Food Science, Plant Science

View Paper: https://www.semanticscholar.org/paper/5a770803e6785e72e64c1559f274a7f5df9cdb75

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Citations in the corpus

Prospecting the characteristics and significance of the phyllosphere microbiome (2018, positive): “…Bacillus Martins et al. (2013) Tamarix Actinomycetales, Bacillales, Halomonas, Halobacteria Finkel et al. (2011) Wolffia australiana Proteobacteria, Bacteroidetes Xie et al. (2015) Agave tequilana Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes Coleman-Derr et al. (2016) Boyle 2006).”
Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture (2018, background): “Likewise, constitutive microbial communities of agave (Coleman-Derr et al., 2016) and cacti (FonsecaGarcía et al.”
Microbial interactions within the plant holobiont (2018, positive): “thaliana [30, 31, 34, 55, 56], and the reciprocal relocation between root- and leafassociated bacterial communities has been further validated using microbiota reconstitution experiments with germ-free A.”
Drought Stress and Root-Associated Bacterial Communities (2018, methodology): “Interestingly, identification of a ‘core microbiome’ of droughtenriched taxa in root endospheres in several different studies (Desgarennes et al., 2014; Coleman-Derr et al., 2016; Naylor et al., 2017) found that these cores contained numerous members of classes Alpha-, Beta-, and Gamma-proteobacteri”
Metacoder: An R package for visualization and manipulation of community taxonomic diversity data (2016, background): “It has been used extensively to explore communities inhabiting diverse environments, including oceans 24 [2], plants [3], animals [4], humans [5], and soil [6].”